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Re: [ferret_users] Having trouble setting up Ferret on Mac - can't save ferret_paths to /usr/local



Hi Cathleen,
Good news! A colleague has built a new version of Ferret, and it can be installed using the same Install script that's used under Unix.

The executable that Markus Pahlow built runs on Leopard (OSX 10.5) and Snow Leopard (OSX 10.6). You can find this from our Downloads page,
http://ferret.pmel.noaa.gov/static/Downloads/ferret_downloads.html

and in particular the MAC for Intel page,
http://ferret.pmel.noaa.gov/static/Downloads/mac_intel_downloads.html

There may be details in the install procecure that we'll need to tweak; apparently Mac uncompresses the tar files when you download them. I've changed the Install script to handle this. If it offers to un-tar them for you as well, it'll probably be easiest to say NO, and let the install procedure take care of that step.

I'll make a formal announcement as well so that all of our Mac users who have been awaiting this will see it.

Ansley

Cathleen Vestfals wrote:
Hello Ferret Users! I am having some issues installing Ferret on my iMac with Snow Leopard 10.6.2
First off, I installed Fink and then proceeded to follow the directions on the Ferret for Mac OS X instruction page. I am using the older version of Ferret (which is supposed to be good for up to 10.5.4). I'm not too computer savvy and didn't want to/know how to do the binary install for 10.6 and build the system.

According to the instructions provided on the Ferret for Mac OS X page, it would be better to use the tcsh shell, however, I couldn't seem to change the startup shell to tcsh (though I tried numerous time through System Preferences/Account/Advanced Options. etc.), so I am stuck using the bash shell. I didn't seem to have a /usr/local directory so I created one using the instructions on the webpage:


In the unlikely event that /usr/local does not exist, please make it, and give "other" read and execute permissions (in my case, using the bash shell):

sudo bash
mkdir /usr/local
chmod go+rx /usr/local

I then followed the directions to install Ferret:
sudo bash
cd /usr/local
tar zxvf ~/Desktop/ferret.tgz

The Ferret download is now located in /usr/local/ferret

I was trying to fix the ferret_paths file as per the instructions on the bottom of the webpage by using the /usr/local/ferret/bin/ferret_paths_bash_template. I created a .bash_profile and put in the line /usr/local/ferret/bin/ferret_paths in it. However, when I tried to modify the /usr/local/ferret/bin/ferret_paths_bash_template and save it as ferret_paths, it wouldn't let me save it to /usr/local. Apparently I do not have permissions to do that, which is unusual as I am the administrator of my computer. I was trying to modify the template using gedit. Every time I try to save the modified document, I get the message "Could not save the file /usr/local/ferret_paths. You do not have the permissions necessary to save the file. Please check that you typed the location correctly and try again." Recall that this is a message I get in gedit. I am at a loss on how to save this file. I know I can use emacs or something, although when I open that, at the bottom it says "opening direc!
 tory: permission denied, /Users/lclab/.emacs.d/auto-save-list." And I can't figure out how to save things in emacs and get back to the bash - Terminal.

I downloaded gedit to use to modify the ferret_paths template and simply dragged the gedit icon to the applications folder, which is what I was supposed to do, according to the instructions that I downloaded with gedit. I had been using gedit on a NOAA Mac computer when I originally worked with Ferret (but that one had been set up for me by a really smart computer whiz). When I typed gedit into the Terminal, a window opened and I could access and save files using gedit. On the computer that I am using outside of NOAA (I am a graduate student), when I type gedit it says command not found. Do I need to modify some code in my bash startup file? And what is my bash startup file (.bash_profile?) What is the command to get it to understand the gedit command and open gedit from my Terminal session? And how can I get the proper permissions to get gedit to save the file to /usr/local?

Also, now when I am in the / directory and type ls -l, one of the columns has root the whole way down, while the other column says admin and wheel. I am the administrator on this computer, but I don't seem to have any permissions. Please help!!!!


bash-3.2$ ls -l
total 36525
drwxrwxr-x+ 37 	root  admin      1258 Jan  5 13:50 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  5 	root  admin       170 Jan  5 13:50 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4107 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64 	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 13 root  wheel       442 Jan  4 17:54 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var


When I used to open a Terminal window, I got:

Last login: Mon Jan  4 17:45:55 on ttys000
-bash: /usr/local/ferret_paths: No such file or directory
catmac:~ lclab$ bash
bash-3.2$ I think I got that message because I couldn't save the modified template because I don't have the proper permissions. I tried to get one of my computer programmer friends to help, but he was at a loss! I am including our session below. I also contacted the very patient, kind, and understanding NOAA computer whiz who instructed me to go into /System/Library/CoreServices and Directory Utility to enable me as the root user, however, no matter what I do, I am unable to save the modified ferret_paths template using gedit to /usr/local.
Now when I open a new Terminal window, I get the message:

Last login: Tue Jan  5 17:41:20 on ttys001
bash
[catmac:~] lclab% bash
bash-3.2$
Somewhere along the line, the message "-bash: /usr/local/ferret_paths: No such file or directory" has disappeared.

I know that many people love Ferret and from what I've managed to do with it (at NOAA), it seems like a great tool, but I am getting extremely frustrated. I would love an easy install for Mac users!!! By the way, if anyone does offer me some assistance in this matter, I am not too familiar with computer lingo and shells and Unix systems, so please, please, please offer suggestions in very basic, easy to follow steps. Like those you would give to a small child as I am not a computer whiz. If this fails....I'm going to have to switch back to R.

Much thanks in advance!!!


I am including my Terminal sessions for anyone that is interested in my struggle!



Last login: Mon Jan  4 17:41:03 on ttys000
bash
-bash: /usr/local/ferret_paths: No such file or directory
catmac:~ lclab$ bash
bash-3.2$ cd ..
bash-3.2$ ls
Shared	lclab
bash-3.2$ sudo chown root:admin /
Password:
bash-3.2$ ls -l
total 0
drwxrwxrwt   4 root   wheel   136 Dec 17 11:33 Shared
drwxr-xr-x+ 30 lclab  staff  1020 Jan  4 17:35 lclab
bash-3.2$ cd lclab
bash-3.2$ ls
Desktop			Movies			Send Registration
Documents		Music			Sites
Downloads		Pictures		fink-0.29.10
Library			Public
bash-3.2$ cd /usr
bash-3.2$ ls -l
total 8
drwxr-xr-x     8 	root  wheel    272 Nov 19 20:55 X11
lrwxr-xr-x     1 	root  wheel      3 Nov 19 20:55 X11R6 -> X11
drwxr-xr-x  1068 	root  wheel  36312 Dec 22 16:05 bin
drwxr-xr-x   271 	root  wheel   9214 Dec 22 16:03 include
drwxr-xr-x   383 	root  wheel  13022 Dec 22 16:04 lib
drwxr-xr-x   103 	root  wheel   3502 Dec 22 16:04 libexec
drwxr-xr-x     3 	root  wheel    102 Jan  4 14:13 local
drwxr-xr-x   236 	root  wheel   8024 Dec 22 16:04 sbin
drwxr-xr-x    74 	root  wheel   2516 Dec 22 16:04 share
drwxr-xr-x     4 	root  wheel    136 Nov 19 20:44 standalone
bash-3.2$ cd ..
bash-3.2$ sudo chown root:admin /
bash-3.2$ xxxxxx
bash: xxxxxx: event not found
bash-3.2$ sudo chown root:admin /
bash-3.2$ ls
Applications			etc
Developer			home
Library				mach_kernel
Network				net
System				private
User Guides And Information	sbin
Users				sw
Volumes				tmp
bin				usr
cores				var
dev
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 	root  admin      1258 Jan  4 14:23 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  4 	root  admin       136 Jan  4 17:36 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4080 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64 	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxr-xr-x@ 12 	root  wheel       408 Jan  4 14:12 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var
bash-3.2$ cd usr
bash-3.2$ ls
X11		bin		lib		local		share
X11R6		include		libexec		sbin		standalone
bash-3.2$ mkdir temp
mkdir: temp: Permission denied
bash-3.2$ su
Password:
su: Sorry
bash-3.2$ bash-3.2$ bash-3.2$ ls -l
total 8
drwxr-xr-x     8 	root  wheel    272 Nov 19 20:55 X11
lrwxr-xr-x     1 	root  wheel      3 Nov 19 20:55 X11R6 -> X11
drwxr-xr-x  1068 	root  wheel  36312 Dec 22 16:05 bin
drwxr-xr-x   271 	root  wheel   9214 Dec 22 16:03 include
drwxr-xr-x   383 	root  wheel  13022 Dec 22 16:04 lib
drwxr-xr-x   103 	root  wheel   3502 Dec 22 16:04 libexec
drwxr-xr-x     3 	root  wheel    102 Jan  4 14:13 local
drwxr-xr-x   236 	root  wheel   8024 Dec 22 16:04 sbin
drwxr-xr-x    74 	root  wheel   2516 Dec 22 16:04 share
drwxr-xr-x     4 	root  wheel    136 Nov 19 20:44 standalone
bash-3.2$ cd ..
bash-3.2$ ls
Applications			etc
Developer			home
Library				mach_kernel
Network				net
System				private
User Guides And Information	sbin
Users				sw
Volumes				tmp
bin				usr
cores				var
dev
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 	root  admin      1258 Jan  4 14:23 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  4 	root  admin       136 Jan  4 17:36 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4080 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64 	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxr-xr-x@ 12 	root  wheel       408 Jan  4 14:12 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var
bash-3.2$ chmod 777 usr
chmod: Unable to change file mode on usr: Operation not permitted
bash-3.2$ sudo chmod 777 usr
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 	root  admin      1258 Jan  4 14:23 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  4 	root  admin       136 Jan  4 17:36 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4080 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64 	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 12 root  wheel       408 Jan  4 14:12 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var
bash-3.2$ cd usr
bash-3.2$ mkdir tttt
bash-3.2$ rd tttt
bash: rd: command not found
bash-3.2$ rmdir tttt
bash-3.2$ ls -l
total 8
drwxr-xr-x     8 	root  wheel    272 Nov 19 20:55 X11
lrwxr-xr-x     1 	root  wheel      3 Nov 19 20:55 X11R6 -> X11
drwxr-xr-x  1068 	root  wheel  36312 Dec 22 16:05 bin
drwxr-xr-x   271 	root  wheel   9214 Dec 22 16:03 include
drwxr-xr-x   383 	root  wheel  13022 Dec 22 16:04 lib
drwxr-xr-x   103 	root  wheel   3502 Dec 22 16:04 libexec
drwxr-xr-x     3 	root  wheel    102 Jan  4 14:13 local
drwxr-xr-x   236 	root  wheel   8024 Dec 22 16:04 sbin
drwxr-xr-x    74 	root  wheel   2516 Dec 22 16:04 share
drwxr-xr-x     4	root  wheel    136 Nov 19 20:44 standalone
bash-3.2$ cd ..
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 	root  admin      1258 Jan  4 14:23 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  4 	root  admin       136 Jan  4 17:36 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4080 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64 	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 12 root  wheel       408 Jan  4 17:50 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var
bash-3.2$ sudo chmod 755 usr
bash-3.2$ ls -l
total 36524
drwxrwxr-x+ 37 	root  admin      1258 Jan  4 14:23 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  4 	root  admin       136 Jan  4 17:36 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4080 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxr-xr-x@ 12 	root  wheel       408 Jan  4 17:50 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var
bash-3.2$ cd usr
bash-3.2$ mkdir temp
mkdir: temp: Permission denied
bash-3.2$ cd ..
bash-3.2$ sudo chmod 777 usr
bash-3.2$ whoami
lclab
bash-3.2$ cd usr
bash-3.2$ bash-3.2$ bash-3.2$ bash-3.2$ mkdir temp
bash-3.2$ cd ..
bash-3.2$ gedit
bash: gedit: command not found
bash-3.2$ sudo chmod 777 usr
Password:
bash-3.2$ rmdir usr
rmdir: usr: Permission denied
bash-3.2$ chgrp admin usr
chgrp: usr: Operation not permitted
bash-3.2$ chown lclab usr
chown: usr: Operation not permitted
bash-3.2$ ls -l
total 36525
drwxrwxr-x+ 37 	root  admin      1258 Jan  5 13:50 Applications
drwxrwxr-x@ 15 	root  admin       510 Dec 22 16:02 Developer
drwxrwxr-t+ 57 	root  admin      1938 Jan  4 17:25 Library
drwxr-xr-x@  2 	root  wheel        68 Oct  4 21:42 Network
drwxr-xr-x   4 	root  wheel       136 Nov 19 20:45 System
lrwxr-xr-x   1 		root  admin        60 Dec 17 11:12 User Guides And Information -> /Library/Documentation/User Guides and Information.localized
drwxr-xr-x   5 	root  admin       170 Dec 17 11:12 Users
drwxrwxrwt@  5 	root  admin       170 Jan  5 13:50 Volumes
drwxr-xr-x@ 39 	root  wheel      1326 Nov 19 20:44 bin
drwxrwxr-t@  2 	root  admin        68 Oct  4 21:42 cores
dr-xr-xr-x   3 		root  wheel      4107 Jan  4 17:36 dev
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 etc -> private/etc
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 home
-rw-r--r--@  1 	root  wheel  18676624 Nov  3 23:10 mach_kernel
dr-xr-xr-x   2 		root  wheel         1 Jan  4 17:36 net
drwxr-xr-x@  6 	root  wheel       204 Nov 19 20:46 private
drwxr-xr-x@ 64 	root  wheel      2176 Nov 19 20:44 sbin
drwxr-xr-x  11 	root  admin       374 Dec 22 16:20 sw
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 tmp -> private/tmp
drwxrwxrwx@ 13 root  wheel       442 Jan  4 17:54 usr
lrwxr-xr-x@  1 	root  wheel        11 Nov 19 20:44 var -> private/var
bash-3.2$ pwd
/
bash-3.2$




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